Examples with SampleMaterial de.symeda.sormas.api.sample.SampleMaterial used on opensource projects

Example 1 with SampleMaterial

use of de.symeda.sormas.api.sample.SampleMaterial in project SORMAS-Project by hzi-braunschweig.

the class SampleFacadeEjb method getSimilarSamples.

@Override
public List<SampleDto> getSimilarSamples(SampleSimilarityCriteria criteria) {
    final CriteriaBuilder cb = em.getCriteriaBuilder();
    final CriteriaQuery<Sample> cq = cb.createQuery(Sample.class);
    final Root<Sample> root = cq.from(Sample.class);
    cq.distinct(true);
    SampleJoins<Sample> joins = new SampleJoins<>(root);
    SampleCriteria sampleCriteria = new SampleCriteria();
    sampleCriteria.caze(criteria.getCaze()).contact(criteria.getContact()).eventParticipant(criteria.getEventParticipant());
    Predicate filter = sampleService.createUserFilter(cq, cb, joins, sampleCriteria);
    filter = CriteriaBuilderHelper.and(cb, filter, sampleService.buildCriteriaFilter(sampleCriteria, cb, joins));
    Predicate similarityFilter = null;
    if (criteria.getLabSampleId() != null) {
        similarityFilter = cb.equal(root.get(Sample.LAB_SAMPLE_ID), criteria.getLabSampleId());
    }
    Date sampleDateTime = criteria.getSampleDateTime();
    SampleMaterial sampleMaterial = criteria.getSampleMaterial();
    if (sampleDateTime != null && sampleMaterial != null) {
        Predicate dateAndMaterialFilter = cb.and(cb.between(root.get(Sample.SAMPLE_DATE_TIME), DateHelper.getStartOfDay(DateHelper.subtractDays(sampleDateTime, SIMILARITY_DATE_TIME_THRESHOLD)), DateHelper.getEndOfDay(DateHelper.addDays(sampleDateTime, SIMILARITY_DATE_TIME_THRESHOLD))), cb.equal(root.get(Sample.SAMPLE_MATERIAL), sampleMaterial));
        similarityFilter = CriteriaBuilderHelper.or(cb, similarityFilter, dateAndMaterialFilter);
    }
    filter = CriteriaBuilderHelper.and(cb, filter, similarityFilter);
    if (filter != null) {
        cq.where(filter);
    }
    List<Sample> samples = em.createQuery(cq).getResultList();
    if (samples.size() == 0 && (sampleDateTime == null || sampleMaterial == null)) {
        return getByCriteria(sampleCriteria);
    }
    Pseudonymizer pseudonymizer = Pseudonymizer.getDefault(userService::hasRight);
    return samples.stream().map(s -> convertToDto(s, pseudonymizer)).collect(Collectors.toList());
}

Example 2 with SampleMaterial

use of de.symeda.sormas.api.sample.SampleMaterial in project SORMAS-Project by hzi-braunschweig.

the class DevModeView method createSamplesGeneratorLayout.

private VerticalLayout createSamplesGeneratorLayout() {
    VerticalLayout sampleGeneratorLayout = new VerticalLayout();
    sampleGeneratorLayout.setMargin(false);
    sampleGeneratorLayout.setSpacing(false);
    Label heading = new Label(I18nProperties.getCaption(Captions.devModeGenerateSamples));
    CssStyles.style(heading, CssStyles.H2);
    sampleGeneratorLayout.addComponent(heading);
    HorizontalLayout sampleOptionsFirstLineLayout = new HorizontalLayout();
    TextField sampleCountField = new TextField();
    sampleCountField.setCaption(I18nProperties.getCaption(Captions.devModeSampleCount));
    sampleGeneratorConfigBinder.forField(sampleCountField).withConverter(new StringToIntegerConverter("Must be a number")).bind(SampleGenerationConfig::getSampleCount, SampleGenerationConfig::setSampleCount);
    sampleOptionsFirstLineLayout.addComponent(sampleCountField);
    DateField startDateField = new DateField();
    startDateField.setCaption(I18nProperties.getCaption(Captions.devModeSampleStartDate));
    startDateField.setDateFormat(DateFormatHelper.getDateFormatPattern());
    startDateField.setLenient(true);
    sampleGeneratorConfigBinder.bind(startDateField, SampleGenerationConfig::getStartDate, SampleGenerationConfig::setStartDate);
    sampleOptionsFirstLineLayout.addComponent(startDateField);
    DateField endDateField = new DateField();
    endDateField.setCaption(I18nProperties.getCaption(Captions.devModeSampleEndDate));
    endDateField.setDateFormat(DateFormatHelper.getDateFormatPattern());
    endDateField.setLenient(true);
    sampleGeneratorConfigBinder.bind(endDateField, SampleGenerationConfig::getEndDate, SampleGenerationConfig::setEndDate);
    sampleOptionsFirstLineLayout.addComponent(endDateField);
    ComboBox<Disease> diseaseField = new ComboBox<>(null, FacadeProvider.getDiseaseConfigurationFacade().getAllDiseases(true, true, true));
    diseaseField.setCaption(I18nProperties.getCaption(Captions.devModeSampleDisease));
    sampleGeneratorConfigBinder.bind(diseaseField, SampleGenerationConfig::getDisease, SampleGenerationConfig::setDisease);
    diseaseField.setRequiredIndicatorVisible(true);
    sampleOptionsFirstLineLayout.addComponent(diseaseField);
    List<RegionReferenceDto> regions = FacadeProvider.getRegionFacade().getAllActiveByServerCountry();
    ComboBox<RegionReferenceDto> regionField = new ComboBox<>(null, regions);
    regionField.setCaption(I18nProperties.getCaption(Captions.devModeSampleRegion));
    sampleGeneratorConfigBinder.bind(regionField, SampleGenerationConfig::getRegion, SampleGenerationConfig::setRegion);
    sampleOptionsFirstLineLayout.addComponent(regionField);
    ComboBox<DistrictReferenceDto> districtField = new ComboBox<>();
    districtField.setCaption(I18nProperties.getCaption(Captions.devModeSampleDistrict));
    sampleGeneratorConfigBinder.bind(districtField, SampleGenerationConfig::getDistrict, SampleGenerationConfig::setDistrict);
    sampleOptionsFirstLineLayout.addComponent(districtField);
    regionField.addValueChangeListener(event -> {
        RegionReferenceDto region = event.getValue();
        if (region != null) {
            districtField.setItems(FacadeProvider.getDistrictFacade().getAllActiveByRegion(region.getUuid()));
        } else {
            districtField.setItems(new ArrayList<DistrictReferenceDto>());
        }
    });
    Button generateButton = ButtonHelper.createButton(I18nProperties.getCaption(Captions.devModeGenerateSamples), e -> generateSamples(), CssStyles.FORCE_CAPTION);
    sampleOptionsFirstLineLayout.addComponent(generateButton);
    sampleGeneratorLayout.addComponent(sampleOptionsFirstLineLayout);
    HorizontalLayout sampleOptionsSecondLineLayout = new HorizontalLayout();
    ComboBox<SampleMaterial> sampleMaterial = new ComboBox(null, Arrays.asList(SampleMaterial.values()));
    sampleMaterial.setCaption(I18nProperties.getCaption(Captions.devModeSampleMaterial));
    sampleGeneratorConfigBinder.bind(sampleMaterial, SampleGenerationConfig::getSampleMaterial, SampleGenerationConfig::setSampleMaterial);
    sampleMaterial.setRequiredIndicatorVisible(true);
    sampleOptionsSecondLineLayout.addComponent(sampleMaterial);
    ComboBox<FacilityReferenceDto> laboratory = new ComboBox(null, FacadeProvider.getFacilityFacade().getAllActiveLaboratories(true));
    laboratory.setCaption(I18nProperties.getCaption(Captions.devModeSampleLaboratory));
    sampleGeneratorConfigBinder.bind(laboratory, SampleGenerationConfig::getLaboratory, SampleGenerationConfig::setLaboratory);
    laboratory.setRequiredIndicatorVisible(true);
    sampleOptionsSecondLineLayout.addComponent(laboratory);
    sampleGeneratorLayout.addComponent(sampleOptionsSecondLineLayout);
    HorizontalLayout sampleOptionsThirdLineLayout = new HorizontalLayout();
    CheckBox externalLabTesting = new CheckBox(I18nProperties.getCaption(Captions.devModeSampleExternalLabTesting));
    sampleGeneratorConfigBinder.bind(externalLabTesting, SampleGenerationConfig::isExternalLabOrInternalInHouseTesting, SampleGenerationConfig::setExternalLabOrInternalInHouseTesting);
    externalLabTesting.setValue(true);
    sampleOptionsThirdLineLayout.addComponent(externalLabTesting);
    CheckBox requestPathogenTestsToBePerformed = new CheckBox(I18nProperties.getCaption(Captions.devModeSamplePathogenTestsToBePerformed));
    sampleGeneratorConfigBinder.bind(requestPathogenTestsToBePerformed, SampleGenerationConfig::isRequestPathogenTestsToBePerformed, SampleGenerationConfig::setRequestPathogenTestsToBePerformed);
    sampleOptionsThirdLineLayout.addComponent(requestPathogenTestsToBePerformed);
    CheckBox requestAdditionalTestsToBePerformed = new CheckBox(I18nProperties.getCaption(Captions.devModeSampleAdditionalTestsToBePerformed));
    sampleGeneratorConfigBinder.bind(requestAdditionalTestsToBePerformed, SampleGenerationConfig::isRequestAdditionalTestsToBePerformed, SampleGenerationConfig::setRequestAdditionalTestsToBePerformed);
    sampleOptionsThirdLineLayout.addComponent(requestAdditionalTestsToBePerformed);
    CheckBox sendDispatch = new CheckBox(I18nProperties.getCaption(Captions.devModeSampleSendDispatch));
    sampleGeneratorConfigBinder.bind(sendDispatch, SampleGenerationConfig::isSendDispatch, SampleGenerationConfig::setSendDispatch);
    sampleOptionsThirdLineLayout.addComponent(sendDispatch);
    CheckBox received = new CheckBox(I18nProperties.getCaption(Captions.devModeSampleReceived));
    sampleGeneratorConfigBinder.bind(received, SampleGenerationConfig::isReceived, SampleGenerationConfig::setReceived);
    sampleOptionsThirdLineLayout.addComponent(received);
    externalLabTesting.addValueChangeListener(event -> {
        if (externalLabTesting.getValue()) {
            requestPathogenTestsToBePerformed.setVisible(true);
            sendDispatch.setVisible(true);
            received.setVisible(true);
            laboratory.setVisible(true);
            sampleGenerationConfig.setSamplePurpose(SamplePurpose.EXTERNAL);
        } else {
            requestPathogenTestsToBePerformed.setVisible(false);
            sendDispatch.setVisible(false);
            received.setVisible(false);
            laboratory.setVisible(false);
            sampleGenerationConfig.setSamplePurpose(SamplePurpose.INTERNAL);
        }
    });
    sampleGeneratorLayout.addComponent(sampleOptionsThirdLineLayout);
    sampleGenerationConfig.setRegion(regions.get(0));
    sampleGenerationConfig.setDistrict(FacadeProvider.getDistrictFacade().getAllActiveByRegion(sampleGenerationConfig.getRegion().getUuid()).get(0));
    sampleGeneratorConfigBinder.setBean(sampleGenerationConfig);
    return sampleGeneratorLayout;
}

Example 3 with SampleMaterial

use of de.symeda.sormas.api.sample.SampleMaterial in project SORMAS-Project by hzi-braunschweig.

the class TestEntityCreator method createSample.

public static Sample createSample(Case caze) {
    if (caze == null) {
        caze = createCase();
    }
    Date sampleDateTime = DateHelper.subtractDays(new Date(), 1);
    Facility lab = DatabaseHelper.getFacilityDao().queryForAll().get(0);
    SampleMaterial material = SampleMaterial.BLOOD;
    Sample sample = DatabaseHelper.getSampleDao().build(caze);
    sample.setSampleDateTime(sampleDateTime);
    sample.setLab(lab);
    sample.setSampleMaterial(material);
    try {
        DatabaseHelper.getSampleDao().saveAndSnapshot(sample);
        DatabaseHelper.getSampleDao().accept(sample);
    } catch (DaoException e) {
        throw new RuntimeException(e);
    }
    return DatabaseHelper.getSampleDao().queryForIdWithEmbedded(sample.getId());
}